Fix the possibility to specify reference files on the command line (#733

)

* fix the possibility to specify reference files on the command line

* update docs

CHANGELOG.md

@@ -51,6 +51,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 -   [#727](https://github.com/SciLifeLab/Sarek/pull/727) - bamQC outputs are no longer overwritten (name of dir is now the file instead of sample)
 -   [#728](https://github.com/SciLifeLab/Sarek/pull/728) - Fix multi sample TSV file [#691](https://github.com/SciLifeLab/Sarek/issues/691)
 -   [#728](https://github.com/SciLifeLab/Sarek/pull/728) - Fix issue with annotation that was consuming `cache` channels
+-   [#733](https://github.com/SciLifeLab/Sarek/pull/733) - Fix the possibility to specify reference files on the command line
 
 ## [2.2.2] - 2018-12-19
 

lib/SarekUtils.groovy

@@ -26,6 +26,10 @@ class SarekUtils {
   // Return element in list of allowed params
   static def checkParams(it) {
     return it in [
+      'ac-loci-GC',
+      'ac-loci',
+      'acLoci',
+      'acLociGC',
       'annotate-tools',
       'annotate-VCF',
       'annotateTools',
@@ -34,21 +38,37 @@ class SarekUtils {
       'awsqueue_tiny',
       'awsqueue',
       'build',
+      'bwa-index',
+      'bwaIndex',
       'call-name',
       'callName',
       'contact-mail',
       'contactMail',
       'container-path',
       'containerPath',
       'containers',
+      'dbsnp-index',
+      'dbsnp',
+      'dbsnpIndex',
       'docker',
       'download',
       'explicit-bqsr-needed',
       'explicitBqsrNeeded',
       'genome_base',
+      'genome-dict',
+      'genome-file',
+      'genome-index',
       'genome',
+      'genomeDict',
+      'genomeFile',
+      'genomeIndex',
       'genomes',
       'help',
+      'intervals',
+      'known-indels-index',
+      'known-indels',
+      'knownIndels',
+      'knownIndelsIndex',
       'local-report-dir',
       'localReportDir',
       'markdup_java_options',
@@ -89,6 +109,8 @@ class SarekUtils {
       'singularity',
       'snp-eff_cache',
       'snpEff_cache',
+      'snpeff-db',
+      'snpeffDb',
       'step',
       'strelka-BP',
       'strelkaBP',
@@ -101,6 +123,8 @@ class SarekUtils {
       'totalMemory',
       'vcflist',
       'vep_cache',
+      'vep-cache-version',
+      'vepCacheVersion',
       'verbose',
       'version']
   }